Starting phenix.real_space_refine
on Fri Jul  3 16:36:33 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7pf5_13368/07_2026/7pf5_13368.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pf5_13368/07_2026/7pf5_13368.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pf5_13368/07_2026/7pf5_13368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pf5_13368/07_2026/7pf5_13368.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pf5_13368/07_2026/7pf5_13368.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pf5_13368/07_2026/7pf5_13368.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     334      5.49       5
     S      10      5.16       5
     C    7420      2.51       5
     N    2528      2.21       5
     O    3178      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13470
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "a"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "b"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "c"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "d"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "e"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "f"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "g"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "h"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "J"
      Number of atoms: 3442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3442
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
    Chain: "I"
      Number of atoms: 3405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3405
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
    Chain: "u"
      Number of atoms: 535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 535
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
  Time building chain proxies: 2.21, per 1000 atoms: 0.16
  Number of scatterers: 13470
  At special positions: 0
  Unit cell: (99.75, 133.35, 126, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     334     15.00
     O    3178      8.00
     N    2528      7.00
     C    7420      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Conformation dependent library (CDL) restraints added in 274.5 milliseconds
  

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1566

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      69.6% alpha, 2.6% beta
      165 base pairs and 284 stacking pairs defined.
    Time for finding SS restraints: 1.52
  Creating SS restraints...
    Processing helix  chain 'a' and resid 44 through 57
    Processing helix  chain 'a' and resid 63 through 79
      removed outlier: 3.568A  pdb=" N   ASP a  77 " --> pdb=" O   GLU a  73 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   PHE a  78 " --> pdb=" O   ILE a  74 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 85 through 114
    Processing helix  chain 'a' and resid 120 through 132
      removed outlier: 3.549A  pdb=" N   ILE a 124 " --> pdb=" O   MET a 120 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 24 through 29
    Processing helix  chain 'b' and resid 30 through 42
    Processing helix  chain 'b' and resid 49 through 77
      removed outlier: 4.024A  pdb=" N   GLU b  53 " --> pdb=" O   LEU b  49 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 82 through 93
      removed outlier: 3.566A  pdb=" N   GLN b  93 " --> pdb=" O   ALA b  89 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 16 through 22
    Processing helix  chain 'c' and resid 26 through 37
    Processing helix  chain 'c' and resid 45 through 73
      removed outlier: 4.247A  pdb=" N   VAL c  49 " --> pdb=" O   ALA c  45 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 79 through 89
    Processing helix  chain 'c' and resid 90 through 97
    Processing helix  chain 'd' and resid 37 through 49
    Processing helix  chain 'd' and resid 55 through 84
    Processing helix  chain 'd' and resid 90 through 102
    Processing helix  chain 'd' and resid 103 through 123
    Processing helix  chain 'e' and resid 44 through 57
    Processing helix  chain 'e' and resid 63 through 77
      removed outlier: 3.555A  pdb=" N   ASP e  77 " --> pdb=" O   GLU e  73 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 85 through 114
    Processing helix  chain 'e' and resid 120 through 132
    Processing helix  chain 'f' and resid 30 through 41
    Processing helix  chain 'f' and resid 49 through 76
      removed outlier: 3.951A  pdb=" N   GLU f  53 " --> pdb=" O   LEU f  49 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ASP f  68 " --> pdb=" O   ASN f  64 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 82 through 93
      removed outlier: 3.572A  pdb=" N   GLN f  93 " --> pdb=" O   ALA f  89 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 16 through 22
    Processing helix  chain 'g' and resid 26 through 37
    Processing helix  chain 'g' and resid 45 through 73
      removed outlier: 4.020A  pdb=" N   VAL g  49 " --> pdb=" O   ALA g  45 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 79 through 89
      removed outlier: 3.507A  pdb=" N   ASN g  89 " --> pdb=" O   LEU g  85 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 90 through 97
    Processing helix  chain 'h' and resid 37 through 49
      removed outlier: 3.711A  pdb=" N   VAL h  41 " --> pdb=" O   TYR h  37 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 55 through 84
      removed outlier: 3.528A  pdb=" N   ASN h  84 " --> pdb=" O   LEU h  80 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 90 through 102
    Processing helix  chain 'h' and resid 104 through 124
      removed outlier: 3.677A  pdb=" N   LYS h 108 " --> pdb=" O   GLY h 104 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 38 through 51
      removed outlier: 3.991A  pdb=" N   LEU u  42 " --> pdb=" O   PRO u  38 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   SER u  50 " --> pdb=" O   ALA u  46 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LYS u  51 " --> pdb=" O   VAL u  47 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 58 through 69
    Processing helix  chain 'u' and resid 75 through 89
    Processing sheet with id=AA1, first strand: chain 'a' and resid 83 through 84
      removed outlier: 6.871A  pdb=" N   ARG a  83 " --> pdb=" O   VAL b  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'a' and resid 118 through 119
      removed outlier: 3.500A  pdb=" N   ILE a 119 " --> pdb=" O   ARG b  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'c' and resid 42 through 43
      removed outlier: 7.183A  pdb=" N   ARG c  42 " --> pdb=" O   ILE d  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'c' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'e' and resid 83 through 84
      removed outlier: 6.925A  pdb=" N   ARG e  83 " --> pdb=" O   VAL f  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'e' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'g' and resid 42 through 43
      removed outlier: 7.331A  pdb=" N   ARG g  42 " --> pdb=" O   ILE h  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'g' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'u' and resid 56 through 57

    433 hydrogen bonds defined for protein.
    1287 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      423 hydrogen bonds
      846 hydrogen bond angles
      0 basepair planarities
      165 basepair parallelities
      284 stacking parallelities
  Total time for adding SS restraints: 2.39

  Time building geometry restraints manager: 1.41 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 2457
        1.33 -     1.45: 4977
        1.45 -     1.58: 6266
        1.58 -     1.70: 666
        1.70 -     1.82: 20
  Bond restraints: 14386
  Sorted by residual:
  bond pdb=" C3'  DT J 522 "
       pdb=" C2'  DT J 522 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 8.00e-03 1.56e+04 1.74e+01
  bond pdb=" C3'  DG J 463 "
       pdb=" O3'  DG J 463 "
    ideal  model  delta    sigma   weight residual
    1.435  1.386  0.049 1.30e-02 5.92e+03 1.45e+01
  bond pdb=" C3'  DG J 541 "
       pdb=" O3'  DG J 541 "
    ideal  model  delta    sigma   weight residual
    1.435  1.484 -0.049 1.30e-02 5.92e+03 1.44e+01
  bond pdb=" C3'  DG I 335 "
       pdb=" O3'  DG I 335 "
    ideal  model  delta    sigma   weight residual
    1.435  1.484 -0.049 1.30e-02 5.92e+03 1.43e+01
  bond pdb=" C5'  DG I 328 "
       pdb=" C4'  DG I 328 "
    ideal  model  delta    sigma   weight residual
    1.512  1.538 -0.026 7.00e-03 2.04e+04 1.38e+01
  ... (remaining 14381 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 19744
        2.17 -     4.33: 1012
        4.33 -     6.50: 73
        6.50 -     8.67: 18
        8.67 -    10.84: 6
  Bond angle restraints: 20853
  Sorted by residual:
  angle pdb=" O5'  DG I 328 "
        pdb=" C5'  DG I 328 "
        pdb=" C4'  DG I 328 "
      ideal   model   delta    sigma   weight residual
     109.40  113.58   -4.18 8.00e-01 1.56e+00 2.73e+01
  angle pdb=" O4'  DA I 348 "
        pdb=" C4'  DA I 348 "
        pdb=" C3'  DA I 348 "
      ideal   model   delta    sigma   weight residual
     106.00  102.96    3.04 6.00e-01 2.78e+00 2.56e+01
  angle pdb=" O4'  DC J 471 "
        pdb=" C4'  DC J 471 "
        pdb=" C3'  DC J 471 "
      ideal   model   delta    sigma   weight residual
     106.00  103.01    2.99 6.00e-01 2.78e+00 2.49e+01
  angle pdb=" O4'  DC I 279 "
        pdb=" C1'  DC I 279 "
        pdb=" N1   DC I 279 "
      ideal   model   delta    sigma   weight residual
     108.00  111.49   -3.49 7.00e-01 2.04e+00 2.48e+01
  angle pdb=" O4'  DT J 409 "
        pdb=" C4'  DT J 409 "
        pdb=" C3'  DT J 409 "
      ideal   model   delta    sigma   weight residual
     106.00  103.11    2.89 6.00e-01 2.78e+00 2.32e+01
  ... (remaining 20848 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.82: 6119
       35.82 -    71.64: 1652
       71.64 -   107.45: 24
      107.45 -   143.27: 1
      143.27 -   179.09: 3
  Dihedral angle restraints: 7799
    sinusoidal: 5368
      harmonic: 2431
  Sorted by residual:
  dihedral pdb=" CA  TYR e  54 "
           pdb=" C   TYR e  54 "
           pdb=" N   GLN e  55 "
           pdb=" CA  GLN e  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.38   21.62     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  THR d  88 "
           pdb=" C   THR d  88 "
           pdb=" N   ILE d  89 "
           pdb=" CA  ILE d  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.16   19.84     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" C4'  DG I 335 "
           pdb=" C3'  DG I 335 "
           pdb=" O3'  DG I 335 "
           pdb=" P    DT I 336 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.09 -179.09     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 7796 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1573
       0.048 -    0.097: 633
       0.097 -    0.145: 138
       0.145 -    0.193: 23
       0.193 -    0.242: 9
  Chirality restraints: 2376
  Sorted by residual:
  chirality pdb=" C3'  DG I 335 "
            pdb=" C4'  DG I 335 "
            pdb=" O3'  DG I 335 "
            pdb=" C2'  DG I 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.49   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  GLN e  55 "
            pdb=" N   GLN e  55 "
            pdb=" C   GLN e  55 "
            pdb=" CB  GLN e  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CB  ILE d  89 "
            pdb=" CA  ILE d  89 "
            pdb=" CG1 ILE d  89 "
            pdb=" CG2 ILE d  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 2373 not shown)

  Planarity restraints: 1478
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE e  51 "    0.018 2.00e-02 2.50e+03   3.52e-02 1.24e+01
        pdb=" C   ILE e  51 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   ILE e  51 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ARG e  52 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL f  70 "    0.014 2.00e-02 2.50e+03   2.88e-02 8.31e+00
        pdb=" C   VAL f  70 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   VAL f  70 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR f  71 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG d  99 "    0.206 9.50e-02 1.11e+02   9.27e-02 6.37e+00
        pdb=" NE  ARG d  99 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG d  99 "    0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG d  99 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG d  99 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1475 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2832
        2.79 -     3.32: 12441
        3.32 -     3.85: 28918
        3.85 -     4.37: 31999
        4.37 -     4.90: 44664
  Nonbonded interactions: 120854
  Sorted by model distance:
  nonbonded pdb=" O   TYR c  39 "
            pdb=" OG  SER d  78 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" NH2 ARG c  81 "
            pdb=" O   GLN e  55 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" NH1 ARG g  29 "
            pdb=" OE2 GLU h  35 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" ND2 ASN a 108 "
            pdb=" O   GLY b  42 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   THR g  16 "
            pdb=" OG  SER g  19 "
     model   vdw
     2.296 3.040
  ... (remaining 120849 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'a'
  selection = chain 'e'
}
ncs_group {
  reference = chain 'b'
  selection = chain 'f'
}
ncs_group {
  reference = chain 'c'
  selection = chain 'g'
}
ncs_group {
  reference = chain 'd'
  selection = chain 'h'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.770
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071  14386  Z= 0.604
  Angle     :  1.015  10.836  20853  Z= 0.787
  Chirality :  0.054   0.242   2376
  Planarity :  0.007   0.093   1478
  Dihedral  : 28.940 179.090   6233
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.26), residues: 825
  helix: -0.07 (0.19), residues: 573
  sheet: -0.81 (1.73), residues: 10
  loop : -0.85 (0.34), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG d  99 
 TYR   0.034   0.004   TYR a  54 
 PHE   0.043   0.002   PHE e 104 
 HIS   0.009   0.002   HIS f  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00725 /  0.60 (14386)
  covalent geometry    : angle       1.01487 /  0.79 (20853)
  hydrogen bonds       : bond        0.09845 /  6.54 (  856)
  hydrogen bonds       : angle       4.76893 /  3.48 ( 2133)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: a   54 TYR cc_start: 0.9120 (m-80) cc_final: 0.8696 (m-80)
REVERT: a   79 LYS cc_start: 0.8496 (tmtt) cc_final: 0.8283 (tmtt)
REVERT: a   90 MET cc_start: 0.8857 (mpp) cc_final: 0.8634 (mpp)
REVERT: b   70 VAL cc_start: 0.9567 (t) cc_final: 0.9284 (t)
REVERT: b   85 ASP cc_start: 0.7900 (m-30) cc_final: 0.7677 (m-30)
REVERT: c   30 VAL cc_start: 0.8230 (t) cc_final: 0.8021 (t)
REVERT: c   36 LYS cc_start: 0.8885 (mmpt) cc_final: 0.8596 (mmmt)
REVERT: c   61 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8120 (mt-10)
REVERT: d   65 PHE cc_start: 0.8827 (t80) cc_final: 0.8617 (t80)
REVERT: f   74 GLU cc_start: 0.8709 (pm20) cc_final: 0.8438 (pm20)
REVERT: g   61 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8497 (tm-30)
REVERT: g   62 ILE cc_start: 0.9528 (pt) cc_final: 0.9197 (pt)
REVERT: g   95 LYS cc_start: 0.8892 (tptt) cc_final: 0.8212 (mmmm)
REVERT: h   33 ARG cc_start: 0.6629 (mtp-110) cc_final: 0.6114 (mtt-85)
REVERT: h   51 ASP cc_start: 0.8619 (p0) cc_final: 0.8408 (p0)
REVERT: h  105 GLU cc_start: 0.8526 (tp30) cc_final: 0.8152 (tp30)
REVERT: h  108 LYS cc_start: 0.9413 (ptpt) cc_final: 0.9175 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1022
  time to fit residues: 22.4230
Evaluate side-chains
  103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:   20.0000
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b  75 HIS
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.042235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.034387 restraints weight = 125104.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.035298 restraints weight = 69182.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.035907 restraints weight = 47429.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.036297 restraints weight = 37107.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.036586 restraints weight = 31541.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  14386  Z= 0.167
  Angle     :  0.716   9.861  20853  Z= 0.413
  Chirality :  0.047   0.301   2376
  Planarity :  0.005   0.061   1478
  Dihedral  : 32.350 175.115   4581
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  9.81 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.27), residues: 825
  helix:  0.61 (0.20), residues: 580
  sheet: -0.65 (1.78), residues: 10
  loop : -0.73 (0.35), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG c  42 
 TYR   0.032   0.003   TYR h  83 
 PHE   0.008   0.001   PHE e 104 
 HIS   0.004   0.001   HIS e 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.17 (14386)
  covalent geometry    : angle       0.71621 /  0.41 (20853)
  hydrogen bonds       : bond        0.04818 /  3.27 (  856)
  hydrogen bonds       : angle       3.77170 /  2.77 ( 2133)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 127
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   54 TYR cc_start: 0.8847 (m-80) cc_final: 0.8567 (m-80)
REVERT: a   79 LYS cc_start: 0.8519 (tmtt) cc_final: 0.8072 (tptt)
REVERT: a   80 THR cc_start: 0.7984 (p) cc_final: 0.7566 (p)
REVERT: a   81 ASP cc_start: 0.8524 (p0) cc_final: 0.8007 (p0)
REVERT: a   97 GLU cc_start: 0.7735 (tt0) cc_final: 0.7518 (tt0)
REVERT: b   85 ASP cc_start: 0.7846 (m-30) cc_final: 0.7602 (m-30)
REVERT: b   97 LEU cc_start: 0.8509 (tp) cc_final: 0.8151 (tp)
REVERT: c   36 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8611 (mmmt)
REVERT: d  102 LEU cc_start: 0.9493 (mm) cc_final: 0.9087 (mp)
REVERT: e   97 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8394 (mt-10)
REVERT: e  120 MET cc_start: 0.7335 (mtt) cc_final: 0.7084 (mtt)
REVERT: f   74 GLU cc_start: 0.8367 (pm20) cc_final: 0.7897 (pm20)
REVERT: g   61 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8423 (tm-30)
REVERT: g   62 ILE cc_start: 0.9501 (pt) cc_final: 0.9038 (pt)
REVERT: g   95 LYS cc_start: 0.8811 (tptt) cc_final: 0.8175 (mmmm)
REVERT: h   33 ARG cc_start: 0.6501 (mtp-110) cc_final: 0.5630 (mtt180)
REVERT: h   51 ASP cc_start: 0.8590 (p0) cc_final: 0.8261 (p0)
REVERT: h   85 LYS cc_start: 0.9482 (mppt) cc_final: 0.9277 (mmtm)
REVERT: h  105 GLU cc_start: 0.8602 (tp30) cc_final: 0.8272 (tp30)
REVERT: h  108 LYS cc_start: 0.9337 (ptpt) cc_final: 0.9088 (ptpp)
  outliers start: 5
  outliers final: 5
  residues processed: 130
  average time/residue: 0.1007
  time to fit residues: 18.8766
Evaluate side-chains
  106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   77 ASP
Chi-restraints excluded: chain b residue   68 ASP
Chi-restraints excluded: chain c residue   94 ASN
Chi-restraints excluded: chain c residue  114 VAL
Chi-restraints excluded: chain d residue   52 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 109 optimal weight:   20.0000
   chunk 58 optimal weight:    0.9980
   chunk 17 optimal weight:   20.0000
   chunk 54 optimal weight:    6.9990
   chunk 98 optimal weight:   30.0000
   chunk 64 optimal weight:    0.9990
   chunk 11 optimal weight:    7.9990
   chunk 24 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 108 ASN
** b  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.041997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.034107 restraints weight = 126277.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.035020 restraints weight = 69598.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.035660 restraints weight = 47840.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.036045 restraints weight = 37079.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.036295 restraints weight = 31576.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14386  Z= 0.161
  Angle     :  0.673   9.498  20853  Z= 0.390
  Chirality :  0.044   0.283   2376
  Planarity :  0.005   0.067   1478
  Dihedral  : 32.213 177.562   4581
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.69 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.27), residues: 825
  helix:  0.92 (0.20), residues: 584
  sheet: -0.79 (1.75), residues: 10
  loop : -0.67 (0.35), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG c  29 
 TYR   0.035   0.002   TYR h  83 
 PHE   0.009   0.001   PHE e  78 
 HIS   0.003   0.001   HIS f  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.16 (14386)
  covalent geometry    : angle       0.67275 /  0.39 (20853)
  hydrogen bonds       : bond        0.04728 /  3.19 (  856)
  hydrogen bonds       : angle       3.52434 /  2.59 ( 2133)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   54 TYR cc_start: 0.8829 (m-80) cc_final: 0.8498 (m-80)
REVERT: a   97 GLU cc_start: 0.7753 (tt0) cc_final: 0.7508 (tt0)
REVERT: c   36 LYS cc_start: 0.9028 (mmpt) cc_final: 0.8605 (mmmt)
REVERT: c   61 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: e  120 MET cc_start: 0.7148 (mtt) cc_final: 0.6905 (mtt)
REVERT: f   63 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8658 (mm-30)
REVERT: f   90 LEU cc_start: 0.8814 (mm) cc_final: 0.8590 (mm)
REVERT: g   61 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8458 (tm-30)
REVERT: g   62 ILE cc_start: 0.9516 (pt) cc_final: 0.9118 (pt)
REVERT: g   95 LYS cc_start: 0.8869 (tptt) cc_final: 0.8247 (mmmm)
REVERT: h   33 ARG cc_start: 0.6413 (mtp-110) cc_final: 0.5700 (mtt-85)
REVERT: h   51 ASP cc_start: 0.8571 (p0) cc_final: 0.8264 (p0)
REVERT: h  105 GLU cc_start: 0.8604 (tp30) cc_final: 0.8267 (tp30)
REVERT: h  108 LYS cc_start: 0.9310 (ptpt) cc_final: 0.8894 (ptpp)
  outliers start: 14
  outliers final: 8
  residues processed: 131
  average time/residue: 0.1000
  time to fit residues: 19.0144
Evaluate side-chains
  116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   77 ASP
Chi-restraints excluded: chain c residue   16 THR
Chi-restraints excluded: chain c residue   94 ASN
Chi-restraints excluded: chain c residue  114 VAL
Chi-restraints excluded: chain d residue   52 THR
Chi-restraints excluded: chain d residue  113 GLU
Chi-restraints excluded: chain f residue   74 GLU
Chi-restraints excluded: chain g residue   76 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 109 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 87 optimal weight:   30.0000
   chunk 49 optimal weight:    4.9990
   chunk 95 optimal weight:   20.0000
   chunk 61 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 108 optimal weight:    8.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 108 ASN
** b  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.040772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.032971 restraints weight = 127911.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.033835 restraints weight = 71789.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.034425 restraints weight = 49843.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.034790 restraints weight = 39049.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.035051 restraints weight = 33524.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  14386  Z= 0.209
  Angle     :  0.695  10.463  20853  Z= 0.397
  Chirality :  0.044   0.288   2376
  Planarity :  0.005   0.062   1478
  Dihedral  : 32.216 178.138   4581
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 12.99 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.27), residues: 825
  helix:  1.13 (0.20), residues: 580
  sheet: -0.84 (1.82), residues: 10
  loop : -0.62 (0.36), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG a 131 
 TYR   0.037   0.002   TYR h  83 
 PHE   0.010   0.001   PHE g  25 
 HIS   0.006   0.001   HIS e 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.21 (14386)
  covalent geometry    : angle       0.69478 /  0.40 (20853)
  hydrogen bonds       : bond        0.06208 /  4.20 (  856)
  hydrogen bonds       : angle       3.56781 /  2.62 ( 2133)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   54 TYR cc_start: 0.8821 (m-80) cc_final: 0.8478 (m-80)
REVERT: a   97 GLU cc_start: 0.7726 (tt0) cc_final: 0.7455 (tt0)
REVERT: c   36 LYS cc_start: 0.9086 (mmpt) cc_final: 0.8660 (mmmt)
REVERT: e   97 GLU cc_start: 0.8227 (mt-10) cc_final: 0.8023 (mt-10)
REVERT: f   63 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8713 (mm-30)
REVERT: f   90 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8619 (mm)
REVERT: g   61 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8461 (tm-30)
REVERT: g   62 ILE cc_start: 0.9534 (pt) cc_final: 0.9169 (pt)
REVERT: g   95 LYS cc_start: 0.8907 (tptt) cc_final: 0.8215 (mmmm)
REVERT: h   33 ARG cc_start: 0.6577 (mtp-110) cc_final: 0.5662 (mtt-85)
REVERT: h   51 ASP cc_start: 0.8446 (p0) cc_final: 0.8176 (p0)
REVERT: h  105 GLU cc_start: 0.8575 (tp30) cc_final: 0.8303 (tp30)
REVERT: h  108 LYS cc_start: 0.9270 (ptpt) cc_final: 0.8907 (ptpp)
  outliers start: 14
  outliers final: 10
  residues processed: 116
  average time/residue: 0.1061
  time to fit residues: 17.9854
Evaluate side-chains
  110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   77 ASP
Chi-restraints excluded: chain b residue   71 THR
Chi-restraints excluded: chain c residue   16 THR
Chi-restraints excluded: chain c residue   30 VAL
Chi-restraints excluded: chain c residue   94 ASN
Chi-restraints excluded: chain c residue  114 VAL
Chi-restraints excluded: chain d residue   52 THR
Chi-restraints excluded: chain d residue  113 GLU
Chi-restraints excluded: chain f residue   74 GLU
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain g residue   76 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 107 optimal weight:   20.0000
   chunk 28 optimal weight:    1.9990
   chunk 80 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
a  76 GLN
a 108 ASN
** b  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
f  75 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.041501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.033565 restraints weight = 126979.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.034456 restraints weight = 69327.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.035059 restraints weight = 47793.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.035469 restraints weight = 37266.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.035738 restraints weight = 31663.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082  14386  Z= 0.152
  Angle     :  0.668  12.474  20853  Z= 0.381
  Chirality :  0.044   0.351   2376
  Planarity :  0.004   0.059   1478
  Dihedral  : 32.149 177.232   4581
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.42 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.27), residues: 825
  helix:  1.18 (0.20), residues: 588
  sheet: -0.99 (1.74), residues: 10
  loop : -0.56 (0.36), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG c  29 
 TYR   0.039   0.002   TYR h  83 
 PHE   0.020   0.001   PHE d  65 
 HIS   0.003   0.001   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.15 (14386)
  covalent geometry    : angle       0.66762 /  0.38 (20853)
  hydrogen bonds       : bond        0.04270 /  2.93 (  856)
  hydrogen bonds       : angle       3.42929 /  2.53 ( 2133)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   54 TYR cc_start: 0.8790 (m-80) cc_final: 0.8485 (m-80)
REVERT: a   97 GLU cc_start: 0.7769 (tt0) cc_final: 0.7558 (tt0)
REVERT: b   74 GLU cc_start: 0.8949 (pt0) cc_final: 0.8701 (pm20)
REVERT: b   97 LEU cc_start: 0.8896 (tp) cc_final: 0.8693 (tp)
REVERT: c   36 LYS cc_start: 0.9037 (mmpt) cc_final: 0.8614 (mmmt)
REVERT: c   61 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7955 (tm-30)
REVERT: d  120 LYS cc_start: 0.9197 (mtpt) cc_final: 0.8988 (mtpt)
REVERT: f   63 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8605 (mm-30)
REVERT: f   90 LEU cc_start: 0.8783 (mm) cc_final: 0.8565 (mm)
REVERT: g   61 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8481 (tm-30)
REVERT: g   62 ILE cc_start: 0.9540 (pt) cc_final: 0.9164 (pt)
REVERT: g   95 LYS cc_start: 0.8861 (tptt) cc_final: 0.8196 (mmmm)
REVERT: h   33 ARG cc_start: 0.6750 (mtp-110) cc_final: 0.5624 (mtt-85)
REVERT: h   51 ASP cc_start: 0.8466 (p0) cc_final: 0.8179 (p0)
REVERT: h  105 GLU cc_start: 0.8594 (tp30) cc_final: 0.8292 (tp30)
REVERT: h  108 LYS cc_start: 0.9253 (ptpt) cc_final: 0.8912 (ptpp)
REVERT: h  120 LYS cc_start: 0.9429 (mmtm) cc_final: 0.9228 (mmtm)
  outliers start: 12
  outliers final: 8
  residues processed: 126
  average time/residue: 0.1081
  time to fit residues: 19.8702
Evaluate side-chains
  114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   77 ASP
Chi-restraints excluded: chain b residue   71 THR
Chi-restraints excluded: chain c residue   16 THR
Chi-restraints excluded: chain c residue   94 ASN
Chi-restraints excluded: chain c residue  114 VAL
Chi-restraints excluded: chain d residue   52 THR
Chi-restraints excluded: chain d residue  113 GLU
Chi-restraints excluded: chain f residue   74 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0670
   chunk 32 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 95 optimal weight:   20.0000
   chunk 85 optimal weight:   30.0000
   chunk 41 optimal weight:    0.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    0.7522

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** b  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.041853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.033916 restraints weight = 126990.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.034829 restraints weight = 69992.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.035454 restraints weight = 48070.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.035851 restraints weight = 37553.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.036125 restraints weight = 31908.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054  14386  Z= 0.141
  Angle     :  0.662  12.304  20853  Z= 0.377
  Chirality :  0.044   0.434   2376
  Planarity :  0.004   0.057   1478
  Dihedral  : 32.046 177.822   4581
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 15.01 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.28), residues: 825
  helix:  1.18 (0.21), residues: 588
  sheet: -0.98 (1.73), residues: 10
  loop : -0.62 (0.37), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG c  42 
 TYR   0.039   0.002   TYR h  83 
 PHE   0.006   0.001   PHE c  25 
 HIS   0.002   0.001   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.14 (14386)
  covalent geometry    : angle       0.66230 /  0.38 (20853)
  hydrogen bonds       : bond        0.04043 /  2.76 (  856)
  hydrogen bonds       : angle       3.41213 /  2.53 ( 2133)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   54 TYR cc_start: 0.8742 (m-80) cc_final: 0.8534 (m-80)
REVERT: b   74 GLU cc_start: 0.8940 (pt0) cc_final: 0.8646 (pm20)
REVERT: c   36 LYS cc_start: 0.9027 (mmpt) cc_final: 0.8604 (mmmt)
REVERT: d  120 LYS cc_start: 0.9198 (mtpt) cc_final: 0.8987 (mtpt)
REVERT: e   97 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7845 (mt-10)
REVERT: f   63 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8599 (mm-30)
REVERT: f   90 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8545 (mm)
REVERT: g   61 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8497 (tm-30)
REVERT: g   62 ILE cc_start: 0.9531 (pt) cc_final: 0.9157 (pt)
REVERT: g   95 LYS cc_start: 0.8797 (tptt) cc_final: 0.8162 (mmmm)
REVERT: h   33 ARG cc_start: 0.6653 (mtp-110) cc_final: 0.5484 (mtt-85)
REVERT: h   51 ASP cc_start: 0.8598 (p0) cc_final: 0.8316 (p0)
REVERT: h  105 GLU cc_start: 0.8595 (tp30) cc_final: 0.8306 (tp30)
REVERT: h  108 LYS cc_start: 0.9251 (ptpt) cc_final: 0.8909 (ptpp)
  outliers start: 9
  outliers final: 6
  residues processed: 129
  average time/residue: 0.1084
  time to fit residues: 20.5353
Evaluate side-chains
  115 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   77 ASP
Chi-restraints excluded: chain c residue   16 THR
Chi-restraints excluded: chain c residue   94 ASN
Chi-restraints excluded: chain c residue  114 VAL
Chi-restraints excluded: chain d residue  113 GLU
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain g residue   76 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 96 optimal weight:   20.0000
   chunk 98 optimal weight:   30.0000
   chunk 22 optimal weight:    0.9980
   chunk 103 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9980
   chunk 73 optimal weight:   30.0000
   chunk 57 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 90 optimal weight:   20.0000
   chunk 106 optimal weight:   20.0000
   overall best weight:    2.9986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** b  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.040380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.032556 restraints weight = 126851.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.033403 restraints weight = 71487.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.033969 restraints weight = 49857.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.034356 restraints weight = 39334.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.034633 restraints weight = 33691.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  14386  Z= 0.207
  Angle     :  0.700  11.062  20853  Z= 0.393
  Chirality :  0.043   0.333   2376
  Planarity :  0.005   0.060   1478
  Dihedral  : 32.102 177.885   4581
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 16.88 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.28), residues: 825
  helix:  1.17 (0.21), residues: 584
  sheet: -0.66 (1.89), residues: 10
  loop : -0.57 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG b  95 
 TYR   0.043   0.002   TYR h  83 
 PHE   0.011   0.001   PHE g  25 
 HIS   0.015   0.002   HIS e 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.21 (14386)
  covalent geometry    : angle       0.69983 /  0.39 (20853)
  hydrogen bonds       : bond        0.06157 /  4.15 (  856)
  hydrogen bonds       : angle       3.56101 /  2.63 ( 2133)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   54 TYR cc_start: 0.8792 (m-80) cc_final: 0.8548 (m-80)
REVERT: b   97 LEU cc_start: 0.8704 (tp) cc_final: 0.8496 (tp)
REVERT: c   36 LYS cc_start: 0.9103 (mmpt) cc_final: 0.8695 (mmmt)
REVERT: e   97 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7899 (mt-10)
REVERT: f   63 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8587 (mm-30)
REVERT: f   90 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8582 (mm)
REVERT: g   61 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8485 (tm-30)
REVERT: g   62 ILE cc_start: 0.9539 (pt) cc_final: 0.9187 (pt)
REVERT: g   95 LYS cc_start: 0.8881 (tptt) cc_final: 0.8243 (mmmm)
REVERT: h   51 ASP cc_start: 0.8455 (p0) cc_final: 0.8181 (p0)
REVERT: h  105 GLU cc_start: 0.8628 (tp30) cc_final: 0.8349 (tp30)
REVERT: h  108 LYS cc_start: 0.9251 (ptpt) cc_final: 0.8921 (ptpp)
  outliers start: 10
  outliers final: 9
  residues processed: 112
  average time/residue: 0.1132
  time to fit residues: 18.4965
Evaluate side-chains
  111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   77 ASP
Chi-restraints excluded: chain b residue   68 ASP
Chi-restraints excluded: chain b residue   71 THR
Chi-restraints excluded: chain c residue   16 THR
Chi-restraints excluded: chain c residue   94 ASN
Chi-restraints excluded: chain c residue  114 VAL
Chi-restraints excluded: chain d residue  113 GLU
Chi-restraints excluded: chain f residue   22 LEU
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain g residue   76 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 98 optimal weight:   30.0000
   chunk 96 optimal weight:   20.0000
   chunk 20 optimal weight:    0.4980
   chunk 78 optimal weight:   20.0000
   chunk 86 optimal weight:   20.0000
   chunk 24 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 92 optimal weight:   20.0000
   chunk 107 optimal weight:    0.2980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
b  25 ASN
** d  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.041613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.033741 restraints weight = 125987.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.034643 restraints weight = 69592.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.035249 restraints weight = 47822.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.035657 restraints weight = 37519.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.035943 restraints weight = 31839.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  14386  Z= 0.143
  Angle     :  0.666  11.342  20853  Z= 0.378
  Chirality :  0.043   0.372   2376
  Planarity :  0.004   0.057   1478
  Dihedral  : 32.037 177.665   4581
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 18.33 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.28), residues: 825
  helix:  1.24 (0.21), residues: 584
  sheet: -0.72 (1.87), residues: 10
  loop : -0.54 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b  23 
 TYR   0.037   0.002   TYR h  83 
 PHE   0.007   0.001   PHE e 104 
 HIS   0.003   0.001   HIS e 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.14 (14386)
  covalent geometry    : angle       0.66609 /  0.38 (20853)
  hydrogen bonds       : bond        0.03923 /  2.68 (  856)
  hydrogen bonds       : angle       3.44995 /  2.55 ( 2133)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c   36 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8600 (mmmt)
REVERT: c   61 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7872 (tm-30)
REVERT: e   94 GLU cc_start: 0.8461 (tp30) cc_final: 0.8093 (tp30)
REVERT: e   97 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7391 (mp0)
REVERT: f   90 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8506 (mm)
REVERT: g   61 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8508 (tm-30)
REVERT: g   62 ILE cc_start: 0.9534 (pt) cc_final: 0.9166 (pt)
REVERT: g   95 LYS cc_start: 0.8807 (tptt) cc_final: 0.8145 (mmmm)
REVERT: h   51 ASP cc_start: 0.8581 (p0) cc_final: 0.8288 (p0)
REVERT: h  105 GLU cc_start: 0.8617 (tp30) cc_final: 0.8288 (tp30)
REVERT: h  108 LYS cc_start: 0.9243 (ptpt) cc_final: 0.8805 (ptpp)
  outliers start: 10
  outliers final: 8
  residues processed: 117
  average time/residue: 0.1038
  time to fit residues: 18.1834
Evaluate side-chains
  114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   77 ASP
Chi-restraints excluded: chain a residue   97 GLU
Chi-restraints excluded: chain b residue   71 THR
Chi-restraints excluded: chain c residue   16 THR
Chi-restraints excluded: chain c residue   94 ASN
Chi-restraints excluded: chain c residue  114 VAL
Chi-restraints excluded: chain d residue   40 TYR
Chi-restraints excluded: chain d residue  113 GLU
Chi-restraints excluded: chain f residue   90 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 105 optimal weight:    3.9990
   chunk 74 optimal weight:   30.0000
   chunk 75 optimal weight:   20.0000
   chunk 87 optimal weight:   20.0000
   chunk 84 optimal weight:   20.0000
   overall best weight:    1.9986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** b  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.040906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.033053 restraints weight = 128461.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.033945 restraints weight = 71747.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.034524 restraints weight = 49578.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.034928 restraints weight = 39025.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.035209 restraints weight = 33199.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  14386  Z= 0.169
  Angle     :  0.685  15.948  20853  Z= 0.384
  Chirality :  0.043   0.485   2376
  Planarity :  0.004   0.059   1478
  Dihedral  : 32.010 178.307   4581
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 18.47 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.28), residues: 825
  helix:  1.22 (0.21), residues: 582
  sheet: -0.82 (1.81), residues: 10
  loop : -0.44 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG b  39 
 TYR   0.042   0.002   TYR h  83 
 PHE   0.008   0.001   PHE g  25 
 HIS   0.003   0.001   HIS e 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.17 (14386)
  covalent geometry    : angle       0.68550 /  0.38 (20853)
  hydrogen bonds       : bond        0.04950 /  3.34 (  856)
  hydrogen bonds       : angle       3.49684 /  2.56 ( 2133)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c   36 LYS cc_start: 0.9094 (mmpt) cc_final: 0.8683 (mmmt)
REVERT: c   41 GLU cc_start: 0.8176 (pm20) cc_final: 0.7904 (pm20)
REVERT: e   94 GLU cc_start: 0.8419 (tp30) cc_final: 0.8058 (tp30)
REVERT: e   97 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7382 (mp0)
REVERT: f   90 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8540 (mm)
REVERT: g   61 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8502 (tm-30)
REVERT: g   62 ILE cc_start: 0.9535 (pt) cc_final: 0.9176 (pt)
REVERT: g   95 LYS cc_start: 0.8863 (tptt) cc_final: 0.8204 (mmmm)
REVERT: h   51 ASP cc_start: 0.8467 (p0) cc_final: 0.8198 (p0)
REVERT: h  105 GLU cc_start: 0.8581 (tp30) cc_final: 0.8314 (tp30)
REVERT: h  108 LYS cc_start: 0.9239 (ptpt) cc_final: 0.8901 (ptpp)
  outliers start: 9
  outliers final: 7
  residues processed: 112
  average time/residue: 0.1057
  time to fit residues: 17.5406
Evaluate side-chains
  113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   77 ASP
Chi-restraints excluded: chain a residue   97 GLU
Chi-restraints excluded: chain b residue   71 THR
Chi-restraints excluded: chain c residue   16 THR
Chi-restraints excluded: chain c residue   94 ASN
Chi-restraints excluded: chain c residue  114 VAL
Chi-restraints excluded: chain d residue  113 GLU
Chi-restraints excluded: chain f residue   90 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 75 optimal weight:   20.0000
   chunk 6 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 88 optimal weight:   40.0000
   chunk 93 optimal weight:   20.0000
   chunk 100 optimal weight:   20.0000
   chunk 108 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    3.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** d  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
g 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.043139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.035780 restraints weight = 139189.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.036661 restraints weight = 75835.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.037252 restraints weight = 51585.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.037632 restraints weight = 40193.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.037952 restraints weight = 33907.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  14386  Z= 0.225
  Angle     :  0.737  14.087  20853  Z= 0.412
  Chirality :  0.045   0.579   2376
  Planarity :  0.005   0.060   1478
  Dihedral  : 32.212 178.530   4581
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 19.19 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.28), residues: 825
  helix:  1.01 (0.21), residues: 584
  sheet: -0.94 (1.82), residues: 10
  loop : -0.49 (0.38), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG b  23 
 TYR   0.047   0.003   TYR h  83 
 PHE   0.020   0.002   PHE a  84 
 HIS   0.004   0.001   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00442 /  0.23 (14386)
  covalent geometry    : angle       0.73692 /  0.41 (20853)
  hydrogen bonds       : bond        0.07087 /  4.77 (  856)
  hydrogen bonds       : angle       3.73120 /  2.73 ( 2133)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: b   23 ARG cc_start: 0.8058 (pmt170) cc_final: 0.7689 (pmt170)
REVERT: c   36 LYS cc_start: 0.9153 (mmpt) cc_final: 0.8728 (mmmt)
REVERT: c   91 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8288 (tm-30)
REVERT: e   97 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7451 (mt-10)
REVERT: e  120 MET cc_start: 0.7201 (mtt) cc_final: 0.6928 (mmm)
REVERT: f   90 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8772 (mm)
REVERT: g   61 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8446 (tm-30)
REVERT: g   62 ILE cc_start: 0.9503 (pt) cc_final: 0.9130 (pt)
REVERT: g   95 LYS cc_start: 0.8972 (tptt) cc_final: 0.8314 (mmmm)
REVERT: h   51 ASP cc_start: 0.8317 (p0) cc_final: 0.8107 (p0)
REVERT: h  108 LYS cc_start: 0.9141 (ptpt) cc_final: 0.8810 (ptpp)
  outliers start: 9
  outliers final: 8
  residues processed: 108
  average time/residue: 0.1178
  time to fit residues: 18.5189
Evaluate side-chains
  109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   77 ASP
Chi-restraints excluded: chain a residue   97 GLU
Chi-restraints excluded: chain b residue   68 ASP
Chi-restraints excluded: chain c residue   16 THR
Chi-restraints excluded: chain c residue   94 ASN
Chi-restraints excluded: chain c residue  114 VAL
Chi-restraints excluded: chain d residue   40 TYR
Chi-restraints excluded: chain d residue  113 GLU
Chi-restraints excluded: chain f residue   90 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 57 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 74 optimal weight:   30.0000
   chunk 27 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 73 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** d  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.040366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.032544 restraints weight = 128499.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.033401 restraints weight = 71589.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.033983 restraints weight = 49521.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.034387 restraints weight = 38968.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.034661 restraints weight = 33235.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  14386  Z= 0.162
  Angle     :  0.695  15.507  20853  Z= 0.389
  Chirality :  0.044   0.505   2376
  Planarity :  0.004   0.056   1478
  Dihedral  : 32.153 178.687   4581
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 19.48 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.28), residues: 825
  helix:  1.07 (0.21), residues: 582
  sheet:  None (None), residues: 0
  loop : -0.47 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG a  83 
 TYR   0.041   0.002   TYR h  83 
 PHE   0.007   0.001   PHE a  67 
 HIS   0.013   0.001   HIS h 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.16 (14386)
  covalent geometry    : angle       0.69483 /  0.39 (20853)
  hydrogen bonds       : bond        0.04599 /  3.12 (  856)
  hydrogen bonds       : angle       3.60213 /  2.64 ( 2133)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1695.05 seconds
wall clock time: 30 minutes 12.81 seconds (1812.81 seconds total)